CN104849472A - Ultra sensitive method for in situ detection of nucleic acids - Google Patents

Ultra sensitive method for in situ detection of nucleic acids Download PDF

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Publication number
CN104849472A
CN104849472A CN201510204485.0A CN201510204485A CN104849472A CN 104849472 A CN104849472 A CN 104849472A CN 201510204485 A CN201510204485 A CN 201510204485A CN 104849472 A CN104849472 A CN 104849472A
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hrp
nucleic acid
amplicon
tyrasamine
probe
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吴兴永
王晖瑜
苏楠
王力翀
罗宇龄
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Advanced Cell Diagnostics Inc
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Advanced Cell Diagnostics Inc
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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C12Q1/682—Signal amplification
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C12Q1/6818—Hybridisation assays characterised by the detection means involving interaction of two or more labels, e.g. resonant energy transfer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6841—In situ hybridisation

Abstract

Disclosed is a method for in situ detection of one or more target nucleic acids based on a combination of RNAscope TM method and a general ISH signal amplification method. This new method produces high signal intensity and while keeps low background noise of signal amplification. The result can be consistently reproduced and the method can be easily adopted for routine clinic diagnostic use. Further, the invention relates to a kit, comprising the components of RNAscope TM assay and a general ISH signal amplification assay, for sensitive detection of one or more target nucleic acids.

Description

For the ultrasensitive method of in situ detection nucleic acid
Quoting of related application
The application is the applying date is on October 21st, 2011, and application number is 201180062037.1, and denomination of invention is the divisional application of the Chinese invention patent application of " ultrasensitive method in situ detection nucleic acid ".The title that this application claims the attorney docket no.12790-021-888 submitted on October 21st, 2010 is the U.S. Provisional Patent Application the 61/405th of " ultrasensitive method (ULTRA SENSITIVE METHODFOR IN SITU DETECTION OF NUCLEIC ACIDS) in situ detection nucleic acid ", the title of the attorney docket no.12790-022-888 that No. 503 people such as () Wu and on November 10th, 2010 submit to is right of priority and the rights and interests of No. the 61/412nd, 276, U.S. Provisional Patent Application people such as () Wu of " ultrasensitive method (ULTRASENSITIVE METHOD FOR IN SITU DETECTION OF NUCLEIC ACIDS) in situ detection nucleic acid ".Each of these applications is incorporated herein by reference with its full content all for various purposes.
Technical field
Present invention relates in general to nucleic acid chemistry and biochemical measurement.More specifically, the present invention relates to the method analyzing thing in situ detection nucleic acids in samples.
Background technology
In situ hybridization (ISH) is a kind of individual cells, technology of specific nucleic acid molecule in histological tissue section or chromosome preparation of allowing detection and positioning to preserve form.Described this technology first in 1969, and this technology is based on the Complementary hybridization of the specific target sequence of DNA or RNA in nucleotide probe and cell.It can be interior source DNA, mRNA (mRNA), Microrna (miRNA), virus sequence or bacterial sequences.Mark the probe added with reporter molecules, and make binding site visible by fluorescence (fluorescence in situ hybridization, FISH) or colour developing (colour developing in situ hybridization, CISH).
After mankind's genome sequencing completes, in public database and not common database, annotate thousands of individual new people's gene sequence in recent years.Because it has designed and synthesized the antisense probe of the particular sequence for detecting any new gene in cell relatively easily, fast and at an easy rate, therefore this gate new for ISH opens.Can obtain the tissue specificity of gene and cell type specificity expression pattern and expression by ISH, this will provide valuable information for analyzing gene function.
But, due to the sensitivity of ISH technology and specificity poor and DNA or the RNA target of low copy number in cell can not be detected, this can limit their application.It is difficult especially for ISH being applied to clinical criteria, and wherein using formalin to fix and preserving clinical tissue specimen samples with paraffin embedding (FFPE) is the method the most often used in the world.FFPE method saves tissue morphology well, but the accessibility of target sequence and detector probe can be caused poor by the crosslinked fixing of formaldehyde, chemistry between probe molecule and other molecules or structure or Physical interaction poor, and the damage to nucleic acid (especially mRNA).
In order to overcome the restriction of ISH and expand its application in Diagnosis pathology, develop several strategy to improve the sensitivity of ISH.Recently, Advanced Cell Diagnostics, Inc. have developed and is called novel I SH method for amplifying signal (United States Patent (USP) the 7th, 709, No. 198).The oligomeric capture probe that this mensuration comprises unique design and the signal amplifying system be made up of pre-amplicon (preamplifier), amplicon (amplifier) and label probe, thus make it possible to the remarkable amplifying signal when not amplifying background signal, and single rna Molecular Detection can be carried out to almost any gene.Schematically illustrate in FIG the illustrative embodiments of technology and describing in detail in the Part II of the application.
The typical case for detecting target nucleic acid in mensuration, the target mRNA that it is expressed to be detected discharges and by solid surface (such as, the hole of microtiter plate) from cell.Additionally provide one group of two or more capture probe and signal generation polymer.Described capture probe and target nucleic acid and signal produce polymer and hybridize, and therefore signal are produced multimeric capture to target nucleic acid.Described signal produces polymer and comprises label probe (LP).But more generally, except label probe, described signal produces polymer and comprises pre-amplicon and/or amplicon.Described label probe can be bonded to the marking particle or molecule that provide detectable signal.Label probe has the comparatively macromolecular structure making it possible to connect multiple marking particle or molecule, which provides than single marking particle or the stronger signal of molecule.Therefore, improve sensitivity and the specificity of detection of nucleic acids.
But, utilize separately still the wherein RNA that can not reliably detect in the past fixed by the formalin of significantly degrading, some low copy genes in the histotomy of paraffin embedding (FFPE).In addition, use current technology can not make single rna molecule with 40 × amplification developing.Expect to strengthen detection signal further to make it possible to detect any RNA molecule more steadily, comprise the RNA molecule of significantly degraded, and to allow detected RNA signal with 10 × amplify easily video picture.
In this application, we describe novel I SH signal and amplify mensuration to expand the application of ISH in Diagnosis pathology by being merged in a system by two kinds of method for amplifying signal.This system has three kinds of forms: (1) combine with biotin-(streptavidin) avidin, (2) with Antibody Combination, (3) amplify (TSA) with tyramide signal to combine.All these methods can utilize the amplifying power of the specificity that technology is superior and three kinds of amplification methods.We have been surprisingly found that above-mentioned three kinds of composite signal amplification methods significantly can amplify the signal relevant with the existence of target nucleic acid in sample and have excellent signal to noise ratio (S/N ratio) simultaneously.
Based on two kinds of molecules to having very high affinity each other, and an avidin/streptavidin molecule can in conjunction with this fact of four biotin molecules, and biotin-avidin (or biotin-streptavidin) is a kind of known signal amplifying system.Antibody is widely used in signal and amplifies in immunohistochemistry and ISH.TSA is based on the deposition of the multiple haptens tyrasamine molecules by peroxidase activity.Tyrasamine is phenolic compound.When there is a small amount of hydrogen peroxide, the substrate conversion of mark is short (short-lived) of survival period, reactive extremely strong intermediate by immobilized HRP (HRP).Then, superoxide enzyme binding site place or near, the substrate molecule of activation extremely fast react with the electron rich moieties (as tyrosine) of protein and with its covalent bond.By this way, can introduce in hybridization site original position the hapten molecule extra being in a large number bonded to tyrasamine.Subsequently, the tyrasamine-hapten molecule developing of deposition can be made directly or indirectly.
In ISH, employ all these method for amplifying signal and obtain success in various degree, but usually for routine diagnosis pathology, signal intensity and/or signal to noise ratio (S/N ratio) are good not enough.With regard to TSA, particularly, when being used alone in ISH, create a large amount of ground unrests.The consistance in every day and each laboratory does not also reach desired requirement.
Consider above-mentioned situation, need with high strength and the method for amplifying nucleic acid with high specificity.For this method, it is also needed to have the consistance of height.The invention provides these and other features, apparent by reading following content.
Summary of the invention
The present invention will method for amplifying signal and conventional ISH method for amplifying signal be combined as hypersensitization method to detect, quantitatively and one or more target nucleic acids differentiating in sample.Due to the paired capture probe design of its uniqueness, measure and provide superior specificity.By conventional ISH method for amplifying signal (signal such as based on TSA amplifies) is added into measure, this combined method achieves high signal intensity and low background.Be easy to relative with system of method for amplifying signal disclosed in this invention uses and produces consistent result.Method required for protection can easily be suitable for using in routine clinical diagnosis program.
In the preferred embodiment of the present invention, specificity and the sensitivity of disclosed method for amplifying signal is balanced.Reduced by appropriateness the multiple that middle signal amplifies achieves this balance.In one embodiment of the invention, a pre-amplicon is designed in conjunction with 1 to 16 amplicon.In a preferred embodiment, a pre-amplicon is designed in conjunction with 2 to 10 amplicons.In the preferred embodiment of another kind, a pre-amplicon is designed in conjunction with 2 to 5 amplicons.
In the preferred implementation detecting target nucleic acid in sample, first providing package containing or suspect and comprise the sample of described target nucleic acid, and at least one group of two or more capture probe can hybridized with described target nucleic acid, the signal can hybridized to the group of these two or more capture probes produce polymer (wherein said signal produces polymer and comprises label probe) and can be bonded to the signal amplifying probe (wherein said signal amplifying probe comprises label) of described label probe.In the process, first target nucleic acid is hybridized the group to two or more capture probes, then described signal is produced the group of multimeric capture to two or more capture probes described, and whereby described signal is produced multimeric capture to described target nucleic acid.Then, described signal amplifying probe is captured to described label probe, and is captured to described signal generation polymer whereby.In the end in a step, in detection signal amplifying probe label existence, do not exist or measure.
In one embodiment, described signal amplifying probe comprises: the biotin molecule that can be bonded to described label probe, avidin/the streptavidin molecule of described biotin molecule can be bonded to, and be bonded to horseradish peroxidase (HRP), alkaline phosphatase (AP) or fluorophore and the other biotin molecule of avidin/streptavidin molecule can be bonded to.
In another embodiment, described signal amplifying probe comprises: can be bonded to the HRP of described label probe, AP, dinitrophenyl (DNP) or fluorophore molecule, one or more first antibodies of described HRP, AP, DNP or fluorophore molecule can be bonded to, and be bonded to HRP, polymkeric substance-HRP, AP, polymkeric substance-AP or fluorophore and can in conjunction with one or more second antibody of one or more first antibodies described.
In another embodiment, described signal amplifying probe comprises: can be bonded to the HRP molecule of described label probe, multiple can with the tyrasamine-biotin of described HRP molecular reaction or tyrasamine-fluorophore molecule and the certification mark thing that can detect described tyrasamine-biotin or tyrasamine-fluorophore molecule visibly.Described certification mark thing is the combination of avidin/streptavidin-HRP and chromogenic substrate or the combination of avidin/streptavidin-AP and chromogenic substrate.Described chromogenic substrate is selected from: diaminobenzidine (DAB) and fast red.
In one embodiment, described signal produces the label probe that polymer comprises the group can hybridized to two or more capture probes.In another embodiment, described signal produces the amplicon that polymer comprises label probe and hybridizes to described label probe.Described amplicon can hybridize the group to two or more capture probes described.In a preferred embodiment, described signal produces the pre-amplicon that polymer comprises label probe, hybridizes the amplicon of extremely described label and hybridize to one or more amplicons.Described pre-amplicon can hybridize the group to two or more capture probes described.
Described target nucleic acid can be any type, such as, DNA, cDNA, RNA, mRNA, rRNA, miRNA, siRNA and/or etc.
In one embodiment, can amplify on a solid support before hybridizing.
Method of the present invention additionally provides the various ways of Multiple detection (mutiplex) two or more target nucleic acids.Such as, described sample can comprise cell, and described cell comprises or suspects and comprises two or more different target nucleic acids.Described sample can also comprise two or more different cells, and each in described cell comprises or suspects and comprises different target nucleic acids.
Double-color developing in situ hybridization (CISH) or dual FISH (FISH) can be used to detect two kinds of different target nucleic acids.In one embodiment, two kinds of different signal amplifying probes are used to carry out described double-colored CISH, wherein the first signal amplifying probe comprises: tyrasamine-biotin, streptavidin-HRP and DAB, and secondary signal amplifying probe comprises: anti-DNP-AP and fast red.
The present invention includes kit to implement the method.Described kit can comprise reagent and implement the necessary condition of the inventive method to carry out detection of nucleic acids and to provide.Described kit comprises, such as, such kit, it comprises: target nucleic acid, two or more capture probes of can hybridize with described target nucleic acid one group, the signal can hybridized to the group of two or more capture probes produce polymer, wherein said signal produces polymer and comprises label probe, with the signal amplifying probe that can be bonded to described label probe, wherein said signal amplifying probe comprises label.
In the described kit of a type, described signal amplifying probe comprises: the biotin molecule that can be bonded to described label probe, avidin/the streptavidin molecule of described biotin molecule can be bonded to, and be bonded to HRP, AP or fluorophore and the other biotin molecule of avidin/streptavidin molecule can be bonded to.
In the kit of another kind of type, described signal amplifying probe comprises: HRP, AP, DNP or the fluorophore molecule that can be bonded to described label probe, one or more first antibodies of described HRP, AP, DNP or fluorophore molecule can be bonded to, and be bonded to HRP, polymkeric substance-HRP, AP, polymkeric substance-AP or fluorophore and can in conjunction with one or more second antibody of one or more first antibodies described.
In the kit of another kind of type, described signal amplifying probe comprises: can be bonded to the HRP molecule of described label probe, can with multiple tyrasamine-biotin of described HRP molecular reaction or tyrasamine-fluorophore molecule and the certification mark thing that can detect described tyrasamine-biotin molecule visibly.Described certification mark thing can be the combination of avidin/streptavidin-HRP and chromogenic substrate or the combination of avidin/streptavidin-AP and chromogenic substrate.Described chromogenic substrate can be selected from: DAB and fast red.
In a kind of kit, described signal produces the label probe that polymer comprises the group can hybridized to two or more capture probes.In another kind of kit, described signal produces the amplicon that polymer comprises label probe and hybridizes to described label probe.Described amplicon can hybridize the group to two or more capture probes described.In the preferred kit of one, described signal produces the pre-amplicon that polymer comprises label probe, hybridizes the amplicon of extremely described label and hybridize to one or more amplicon.
Pre-amplicon in described kit: the ratio of amplicon can be between 1-16, or is preferably between 2-10 or between 2-5.
Work in the Multiple detection that kit of the present invention can amplify at multiple nucleic acid.Described kit may be used for detecting the nucleic acid target in two or more different cells, and each in described cell comprises or suspects and comprises different target nucleic acids, or detects two or more the nucleic acid targets in a kind of cell.Signal amplifying probe in described kit can be double-color developing in situ hybridization (CISH) probe or dual FISH (FISH) probe.When using double-colored CISH probe, the first signal amplifying probe comprises: tyrasamine-biotin, streptavidin-HRP and DAB, and secondary signal amplifying probe comprises: anti-DNP-AP and fast red.
Definition
Unless otherwise defined, otherwise all technology used herein and scientific terminology have the identical implication general understood with those skilled in the art in the invention.Supplement those definition in the present invention to give a definition and relate to current patent application, and not imputing to any relevant or uncorrelated situation, such as, any patent of owning together or patented claim.Although can use in the practice tested for the present invention and those similar or any methods of being equal to described herein and material, be described herein preferred materials and methods.Therefore, term as used herein only for the object describing embodiment, instead of is intended to restriction.
Term " nucleic acid " (with equivalent terms " polynucleotide ") covers any physical column that can correspond to the monomeric unit of a row nucleotide, it comprises the polymkeric substance of nucleotide (such as, typical DNA or RNA polymkeric substance), peptide nucleic acid (PNA), modify oligonucleotides (such as, comprising biological RNA or DNA is the oligonucleotides of atypical nucleotide, as 2'-O-methylated oligonucleotides) etc.The nucleotide of polynucleotide can be deoxyribonucleotide, ribonucleotide or nucleotide analog, can be natural or non-natural, and can be unsubstituted, unmodified, replace or modify.Described nucleotide can by phosphodiester bond or by connections such as phosphorothioate key, methyl-phosphonate key, boranophosphate ester bonds.Described polynucleotide can comprise non-nucleotide components in addition, as label, quencher, blocking group etc.Described polynucleotide can be (such as) strand or double-strand.
" nucleic acid target " or " target nucleic acid " refer to the nucleic acid that will detect, or optionally its region.
Based on context, " polynucleotide sequence " or " nucleotide sequence " is the polymkeric substance (oligonucleotides, DNA, nucleic acid etc.) of nucleotide or the character string of expression nucleotide polymer.According to any specified polynucleotide sequence, given nucleic acid or complementary polynucleotide sequence (such as, complementary nucleic acid) can be determined.
Broadly use term " gene " to represent any nucleic acid relevant with biological function.Gene generally includes coded sequence and/or expresses the regulating and controlling sequence needed for these coded sequences.Term gene goes for concrete genome sequence and cDNA or mRNA coded by this genome sequence.
Broadly employ term " antibody " in this article and it comprises the antibody of completed assembled, remains the antibody fragment, single-chain antibody, Diabody, antibody chimera, hybrid antibody, bispecific antibody, humanized antibody etc. of the ability of specific binding antigen (such as, Fab, F (ab') 2, Fv and other fragments).Term " antibody " comprises polyclone and monoclonal antibody.
As used herein term " biological sample " or " tissue sample " refer to the sample available from biological experimenter, and it comprises in body or original position obtains, the sample of the biological tissue that touches or collect or liquid source.Biological sample also comprises from before having cancer or the sample in the region of the biological experimenter of cancer cell or tissue.These samples may be, but not limited to, and are separated from mammiferous organ, tissue, part and cell.Exemplary biological samples includes, but not limited to cellular lysate, cell culture, clone, tissue, organ, organelle, biofluid etc.Preferred biological sample includes, but not limited to skin samples, Tissue biopsy samples etc.
Term " label probe " refers to and is directly or indirectly combined with target molecule and makes the entity that described target can be detected by (such as) reading instruments.Label probe (or " LP ") normally comprises one or more single stranded polynucleotide directly or indirectly providing the label of detectable signal.Described label can be covalently attached to described polynucleotide, maybe can configure described polynucleotide with in conjunction with described label (such as, biotinylated polynucleotide can in conjunction with streptavidin mark of correlation thing).Described label probe can (such as) direct cross to target nucleic acid, or it can be hybridized to nucleic acid, and described nucleic acid is hybridized conversely to described target nucleic acid or hybridization to other nucleic acid one or more of having hybridized to described nucleic acid.Therefore, described label probe can comprise the polynucleotide sequence with the polynucleotide sequence complementation of described target nucleic acid, or it can comprise at least one polynucleotide sequence with the polynucleotide sequence complementation in capture probe, amplicon etc.
" label " is the part being conducive to Molecular Detection.In the background of the invention, conventional label comprises fluorescence, luminescence, light scattering and/or colorimetric marker.The label be applicable to comprises enzyme and fluorescing fractions and radioactive nuclide, substrate, co-factor, inhibitor, chemiluminescent moiety, magnetic-particle etc.Exemplary indicia thing comprises: horseradish peroxidase (HRP), alkaline phosphatase (AP), fluorophore, dinitrophenyl (DNP) etc.The patent of the use of these labels is instructed to comprise U.S. Patent No. 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149 and 4,366,241.Multiple label is commercially available and can uses in the background of the invention.
" capture probe " can hybridize to target nucleic acid and label probe is captured to the polynucleotide of this target nucleic acid.Described target-probe can direct cross to described label probe, or it can hybridize to one or more nucleic acid, and described nucleic acid is hybridized to described label probe conversely; Such as, target-probe can be hybridized to amplicon or pre-amplicon.Therefore, described target-probe comprises the second polynucleotide sequence with the first polynucleotide sequence of the polynucleotide sequence complementation of described target nucleic acid and the polynucleotide sequence complementation with described label probe, amplicon, pre-amplicon etc.Preferably, described target-probe is strand.
" amplicon (amplifier) " to hybridize the molecule to multiple label probe, normally polynucleotide.Usually, described amplicon hybridization is to multiple identical label probe.Described amplicon is also hybridized at least one target-probe or is hybridized the nucleic acid be extremely combined with target-probe.Such as, described amplicon can be hybridized at least one target-probe and multiple label probe, or is bonded to pre-amplicon and multiple label probe.Described amplicon can be that (such as) is linear, bifurcated, pectination or branch nucleic acid.Mentioned by all polynucleotide, described amplicon can comprise key and standard deoxyribonucleotide, ribonucleotide and/or phosphodiester bond between the nucleotide of modification and/or off-gauge nucleotide.At (such as) USPN 5,635,352, USPN 5,124,246, USPN 5,710,264 and USPN5,849, describe applicable amplicon in 481.
" pre-amplicon (preamplifier) " is the molecule of the intermediate effect played between one or more target-probe and amplicon, normally polynucleotide.Usually, pre-amplicon is hybridized to one or more target-probe and multiple amplicon simultaneously.At (such as) USPN 5,635,352 and USPN5,681, describe exemplary pre-amplicon in 697.
" ISH " or " in situ hybridization " refers to the complementary DNA of usage flag or a class hybridization of the part of next (original position) position tissue of RNA chain (i.e. probe) or the specific DNA in cutting into slices or RNA sequence.The type of probe is double-stranded DNA (dsDNA), single stranded DNA (ssDNA), single-stranded complementary RNA (sscRNA), mRNA (mRNA), Microrna (miRNA) and synthetic oligonucleotide.
" FISH " or " fluorescence in situ hybridization " refers to the class ISH using fluorescent marker.
" CISH " or " colour developing in situ hybridization " refers to the class ISH using chromogenic label.
" amplification of general purpose I SH signal " measures or system refers to any ISH base in situ hybridization mensuration or the system that can be amplified specific DNA or the RNA sequence of institute's target by described method.It includes, but not limited to disclosed three kinds of exemplary conventional ISH signal amplifying systems (that is, biotinyl ISH, antibody base ISH and TSA base ISH) in the present invention.
Accompanying drawing explanation
Fig. 1 shows the principle measured.Target nucleic acid (as mRNA) and capture probe group are hybridized.Often organize capture probe and comprise two or more capture probes.Described capture probe group and pre-amplicon hybridization.Each pre-amplicon further with multiple amplicon hybridization.One or more label is bonded to, as fluorophore or enzyme by amplicon and multiple label probe are hybridized each label probe of further amplifying signal.Use standard bright-field or epifluorescence microscope detection signal.
Fig. 2 shows the principle that+biotin/(streptavidin) avidin amplifies. in label probe be combined with biotin molecule and be combined with avidin/streptavidin further.Each avidin/streptavidin has the ability in conjunction with maximum 4 biotin molecules, described biotin molecule is bonded to enzyme or fluorescent marker, as horseradish peroxidase (HRP), alkaline phosphatase (AP) or fluorophore, thus the signal of each label probe is caused to increase by 4 times.
Fig. 3 shows the principle that+antibody amplifies. in label probe be bonded to HRP, AP, DNO or fluorophore molecule and identify by the antibody (producing, as goat in A animal kind) of anti-HRP, AP, DNP or fluorophore molecule.Then, the second antibody identification first antibody that can be combined by the HRP of anti-A kind first antibody, polymkeric substance-HRP, AP or polymkeric substance-AP, thus cause the further signal of RNAscope signal to amplify.
Fig. 4 shows the principle that+TSA amplifies. in label probe be bonded to HRP.The label probe that HRP combines impels multiple copies of tyrasamine-biotin or tyrasamine-fluorophore to be covalently bond to the electron rich moieties of the protein of contiguous LP-HRP binding site.Subsequently, tyrasamine-biotin or tyrasamine-fluorophore is detected by avidin/streptavidin-HRP or avidin/streptavidin-AP and to the substrate (as DAB and fast red) of HRP or AP colour developing.Because multiple copies of tyrasamine-biotin can be deposited on around each LP-HRP binding site, therefore significantly improve the intensity of amplifying the final signal of sum as RNAscope amplification and TSA.
The detection of the mRNA of low copy gene HP RT1 during Fig. 5 shows and uses the human breast carcinoma FFPE of RNAscope and RNAscope+TSA program to cut into slices.The signal (right side) obtained by RNAscope+TSA is significantly better than the signal (left side) obtained by means of only RNAscope.
Embodiment
The invention provides the sensitivity that improves and specificity for detecting the method and system of the existence of target nucleic acid in sample.The present invention will method combines with conventional ISH method for amplifying signal (as the method for amplifying signal based on TSA, the method for amplifying signal based on antibody or the method for amplifying signal based on biotin-avidin). method is famous with the high specific of its detection target nucleic acid.In other words, exist target nucleic acid can be detected with high s/n ratio in mensuration.As explained in following part 2, this high specific derives from " two Z " probe design and pre-amplicon-amplicon-label probe signal cascade design.Conventional ISH method for amplifying signal is famous with the ability of the signal amplification of its promotion nucleic acid molecules.But ISH method for amplifying signal is also famous amplifying the high s/n ratio in measuring and be lack of consistency with it.
The present invention will combine with a conventional ISH method for amplifying signal step of going forward side by side of method saves the magnification (amplification ratio) of middle amplicon and pre-amplicon.Except benefit, method and system of the present invention overcomes the shortcoming of conventional ISH method for amplifying signal mentioned above, maintains simultaneously the unique mechanism that middle ground unrest reduces.Therefore, the present invention can reliably detect nucleic acid target with high sensitivity and specificity.Consistance in this good general's of adding detection of nucleic acids result brings up to the level can implemented in diagnostic assay.
1. pass through with the detection of the target nucleic acid of the combination of conventional ISH method for amplifying signal
The invention describes for detecting the novel, simple of target nucleic acid in sample and overdelicate in-situ hybridization method.The method can use in fluorescence ISH (FISH) and colour developing ISH (CISH) measure.The method can detect immobilized nucleic acid (DNA and RNA) in intact cell, histotomy, micro-array tissue and cDNA microarray.
1.1 conventional ISH method for amplifying signal
Develop multiple ISH method for amplifying signal to detect DNA or RNA target.Below by exemplary for description three kinds ISH method for amplifying signal: (1) amplifies based on the ISH signal of biotin-(streptavidin) avidin; (2) the ISH signal based on antibody amplifies, and the ISH signal that (3) amplify (TSA) based on tyramide signal amplifies.Technician is clear can be combined in the present invention use any ISH method for amplifying signal.Therefore, these examples are not regarded as limiting of the invention.
(1) RNAscope+ biotin-(streptavidin) avidin system (Fig. 2).
In one embodiment, based on biotin-(streptavidin) avidin ISH method for amplifying signal with be combined.In one aspect, RNAscope comprises one group of two or more capture probe, multiple label probe, multiple amplicon and multiple pre-amplicon.Target nucleic acid hybridization is to described capture probe group.Then, described capture probe group hybridization is to pre-amplicon.Described pre-amplicon is hybridized further to multiple amplicon.Then, each amplicon hybridization is to multiple label probe.Then, the label probe (LP) of RNAscope composite structure is bonded to the biotin molecule of ISH signal structure for amplifying and forms LP-biotin composite.LP-biotin composite is combined with avidin/streptavidin molecule further.Avidin/streptavidin molecule has the ability in conjunction with maximum 4 biotin molecules, and wherein each biotin molecule is further combined with to HRP or AP.Developing dye (as diaminobenzidine, DAB or fast red) visible detection HRP or AP can be passed through.Therefore, will based on the ISH method for amplifying signal of biotin-(streptavidin) avidin with 4 times are improved in conjunction with making the signal of each label probe.(2) RNAscope+ antibody forming system (Fig. 3).
In another embodiment, based on antibody ISH method for amplifying signal with be combined.In one aspect, RNAscope comprises one group of two or more capture probe, multiple label probe, multiple amplicon and multiple pre-amplicon.Target nucleic acid hybridization is to described capture probe group.The hybridization of two or more capture probes is to nucleic acid target.Each pre-amplicon hybridization to each in two or more capture probes described, each in multiple amplicon hybridization to described pre-amplicon, and the hybridization of multiple label probe is to described amplicon.Each label probe of RNAscope composite structure is bonded to HRP molecule, AP molecule, DNP molecule or fluorophore molecule, and therefore form respectively HRP-LP compound, AP-LP compound, DNP-LP compound or fluorophore-LP compound.Respectively by anti-HRP antibody, anti-AP-LP antibody, anti-DNP-LP antibody or anti-fluorophore-LP antibody recognition HRP-LP, AP-LP, DNP-LP or fluorophore-LP compound.Above-mentioned antibody is produced by animal kind A (as goat).Then, by this first antibody of second antibody identification of anti-kind of A.Described second antibody is combined with HRP, polymkeric substance-HRP, AP, polymkeric substance-AP or fluorophore and can in conjunction with one or more first antibody.Developing dye (as diaminobenzidine (DAB) or fast red) can be passed through and detect HRP or AP visibly.Result of the present invention is that the further signal except RNAscope signal amplifies amplifies.
(3) RNAscope+TSA system (Fig. 4).
In another embodiment, based on TSA ISH method for amplifying signal with be combined.In one aspect, RNAscope comprises one group of two or more capture probe, multiple label probe, multiple amplicon and multiple pre-amplicon.Target nucleic acid hybridization is to described capture probe group.Then, described capture probe group hybridization is to pre-amplicon.Described pre-amplicon is hybridized further to multiple amplicon.Then, each amplicon hybridization is to multiple label probe. each label probe of composite structure is bonded to HRP molecule, thus forms HRP-LP compound.Then, HRP-LP compound is bonded to multiple tyrasamine-biotin or fluorophore-biotin molecule.In this step, HRP-LP compound impels multiple copies of tyrasamine-biotin or fluorophore-biotin to be covalently bond to the electron rich moieties of the protein of contiguous LP-HRP binding site.Subsequently, tyrasamine-biotin or fluorophore-biotin is surveyed by certification mark quality testing.Described certification mark thing is the combination of avidin/streptavidin-HRP and chromogenic substrate or the combination of avidin/streptavidin-AP and chromogenic substrate.HRP or AP on avidin/streptavidin-HRP or avidin/streptavidin-AP compound is detected visibly by chromogenic substrate (as DAB or fast red).Because multiple copies of tyrasamine-biotin or fluorophore-biotin can be deposited on around each LP-HRP binding site, therefore significantly improve the intensity of amplifying the final signal of sum as RNAscope amplification and TSA.
In other embodiments of the ISH method for amplifying signal based on TSA, tyrasamine can also be bonded to other haptens, as digoxin (DIG), trinitrophenyl (TNP), dinitrophenyl (DNP) and fluorescent dye.When using luminescent dye molecule in combining at tyrasamine, directly tyrasamine-dye conjugates can be used for simple and effective fluorescence (FISH) in RNAscope-TSA system and detect.
1.2 improve in the ratio of amplicon/pre-amplicon
Can also finely tune disclosed in this invention with the combination of conventional ISH method for amplifying signal with the sensitivity improving signal and amplify and specificity.This in+conventional ISH method for amplifying signal, main contributions be measure specificity. also provide nucleic acid target target appropriateness signal with high specific to amplify.One of contribution of conventional ISH method for amplifying signal is that their signal strengthens ability (signal boosting power).Therefore, except outside the appropriate signal amplifying power provided, target nucleic acid signal is also amplified to much higher level by conventional ISH method for amplifying signal.
A potential problem is that conventional ISH method for amplifying signal not only amplifies true positives signal, but also amplifies false positive signal.Therefore, the problem that in input, ground unrest raises is faced with the simple combination of conventional ISH method for amplifying signal.The invention discloses a kind of clever method to reduce the level of false positive signal.
Disclosed in this invention with a balance factor of the combination of conventional ISH method for amplifying signal be the size of middle used pre-amplicon.If design is in conjunction with multiple amplicon, then pre-amplicon can be very large molecule.Such as, pre-amplicon can have hybridization to the ability more than 20 amplicons.This large molecule tends to non-specific binding during hybridizing in position in cellular matrix.When in pre-amplicon and sample non-specific binding, multiple identical amplicon and label probe are attracted on it by it, as with target nucleic acid in conjunction with time the same.Be used alone when, the number of the label probe be combined with the pre-amplicon of a small amount of non-specific binding can not produce any observable signal.But, if amplify by the extra of amplifying from the conventional ISH signal of continuous print the signal improving these label probes further, then false positive signal by enough high with thus be detected.
A kind of method reducing this false positive signal reduces the size of pre-amplicon, thus first it is unlikely trapped within cellular matrix; The second, though when it in the sample to which non-specific binding time, also only have a small amount of amplicon molecule to hybridize with it.Therefore, though by conventional ISH signal amplify strengthen signal time, the signal produced by non-specific binding may be too low and can not be detected.In a kind of embodiment of the method, a pre-amplicon design is combined with 1 to 16 amplicon.In preferred embodiment, a pre-amplicon design is combined with 2 to 10 amplicons.In another preferred embodiment, a pre-amplicon design is combined with 2 to 5 amplicons.
In being measured by balance with amplifying power and the specificity of TSA, the original position RNA in routine clinical tissue sample is detected and has achieved best signal to noise ratio (S/N ratio) (see embodiment 1 and Fig. 5).
2. pass through the detection of target nucleic acid
Recently, Advanced Cell Diagnostics, Inc. develops one and is called as powerful in-situ hybridization method (U.S. Patent No. 7,709,198, this patent is incorporated herein by reference with its full content).Due to be a part for method disclosed in the present invention, will describe therefore principle of work to understand the present invention better.
allow the video picture of RNA direct in-situ.The method use oligonucleotide probe group as described below and novel signal amplification system.This mensuration may be used for several samples type, comprises cultured cells, peripheral blood mononuclear cell (PBMC), freezing tissue and formalin is fixed, paraffin embedding (FFPE) tissue.In addition, this mensuration can use colour developing and luciferase assay reagent.
determination techniques provide unicellular in multiple nucleic acid measure (see Fig. 1).The core of this technology is " two Z " probe design, and this design allows the brute force of Specific hybridization signals to amplify, and can not amplify non-specific event simultaneously.Each capture probe (" Z ") has the desired specificities sequence be combined with target mRNA, spacer region and " tail " sequence.Two capture probe (two Z) continuous hybrids are to target mRNA, and two " tail " sequences define 28 base hybridization site of pre-amplicon.Two Z probe design guarantees the high fidelity that signal amplifies, this is because: 1) twin target probe adjacent to each other non-specific hybridization be very impossible to form the binding site of pre-amplicon; With 2) under condition determination, any one tail can be bonded to pre-amplicon separately effectively.The hybridization of pre-amplicon, amplicon and label probe order to each capture probe pair, thus causes every 1kb target RNA to reach 8, the accumulation of 000 labeled molecule.Label probe can be bonded to fluorophore or colour developing enzyme (such as, HRP or AP), thus makes it possible under standard bright-field or TIRF (epifluorescentmicroscope), observe hybridization signal respectively.Use fluorescence labeling probe, signal can containing the fluorescence molecule than conventional RNA fluorescence ISH fado at least 100 times, and be easily visible under standard fluorescent microscope.
In addition, construct multiple signal amplicon, tailer sequence unique in its each identification target-probe, thus make multiple target RNA video picture simultaneously.Importantly, this mensuration is suitable for the RNA of the Partial digestion existed in the FFPE tissue be applicable to, this is because two Z probe is the short region of about 50 nucleotide to target length.
In an example, for detecting target nucleic acid.In the method, the sample comprising one or more cell is provided.The cell tested comprises or suspects and comprises target nucleic acid.Provide in this mensuration: the one group of capture probe comprising two or more capture probes, comprises the label probe of label, and pre-amplicon and amplicon alternatively.
In the method, described capture probe group is hybridized to target nucleic acid in cell.Described label probe is caught into described capture probe group, whereby described label probe is captured to described target nucleic acid.Then, the signal from described label is detected.Because described label is connected with target nucleic acid by capture probe, therefore in cell, the existence of label shows the existence of corresponding nucleic target in cell.Described method is optionally quantitative.Therefore, can the intensity of measuring-signal, and signal intensity can be associated with the amount of target nucleic acid in cell.As another example, can count that quantitative test is carried out to them to the signaling point of each copy of target nucleic acid.
In one aspect, described label probe is directly bonded to described capture probe.In yet another aspect, described label probe is captured to described capture probe indirectly, such as, by the combination of pre-amplicon and/or amplicon.The use of amplicon and pre-amplicon can be favourable in raising signal intensity, this is because they can assist multiple label probe to be bonded to each nucleic acid target.
Although Direct Acquisition Methods and indirect catching method can be used in the technique of the present invention, but preferably indirect catching method, this is because it makes described label probe to become not rely on target, and display the method can be provided better specificity and sensitivity by other disclosures.
? in mensuration, described capture probe is custom-designed.In each capture probe, there is the part T of the partial complementarity at least one and target molecule, and with another the part L of the partial complementarity on label probe.T with L part is connected by part C.Indirectly catching in embodiment, two adjacent capture probes are incorporated into target be concerned about in the probe groups of gene.T1 and T2 designs with two uniquenesses on target nucleic acid and adjacent partial complementarity.L1 with L2 can be different or identical, and two adjacent part complementations on they and label probe.Their bound fraction T, L or both designs make the connection between label probe and target be unstable, and when only have in capture probe one in place time, they tend under hybridization temperature be separated.This design should be able to make it have extraordinary specificity, this is because when two independent capture probes all identify target and be combined with flanking sequence or with target gene closely time, signal produces label probe only can be connected to be concerned about target gene.In one embodiment, the melting temperature T of the T part of two capture probes mdesign is significantly higher than hybridization temperature, simultaneously the T of L part mlower than hybridization temperature.Therefore, hybridizing period T part strongly and be stably bonded to target molecule, and when only having one to exist in capture probe, L part is faint and be bonded to label probe astatically.But, when two capture probes all exist, L1 and L2 be combined in hybridization during strongly and stably keep label probe.Such as, the length of T part can be 20-30 nucleotide, and the length of L part is 13-15 nucleotide; The length of C can be 0 to 10 nucleotide, such as, 5 nucleotide.In another embodiment, the T of T part mlower than hybridization temperature, and the T of L part mbe significantly higher than hybridization temperature.In the same way, only have when two capture probes are all hybridized to target with cooperation mode, the connection between label probe and target just can retain during hybridizing.For other detailed contents of capture probe design, see U.S. Patent No. 7,709,198.
In the embodiment of above kind, capture probe is preferably hybridized to nonoverlapping polynucleotide sequence in they corresponding nucleic acid targets.Capture probe can cover (but not needing) nucleic acid target target neighboring region.Optionally provide for the blocking-up probe as the polynucleotide of hybridizing to the nucleic acid targeting regions do not occupied by target-probe, and described blocking-up Probe Hybridization is to described target.For given nucleic acid target, corresponding capture probe and block probe preferably with nucleic acid target in physically separated, nonoverlapping complementary, described nonoverlapping sequence preferably (but not must) is adjacent.In some embodiments, make capture probe and optional blocking-up probe is adjacent to each other can improve intensity for hybridization, removing secondary structure, and guarantee more unanimously and repeatably signal.
In the detection of cell amplifying nucleic acid target, usually before the hybridization of capture probe by cell fixing and permeability described nucleic acid target to be retained in cell and to allow capture probe, label probe etc. to enter cell.Alternatively, cell is cleaned to remove the material be not captured on one of described nucleic acid target.Such as, after any number of step, in capture probe and nucleic acid target hybridization with after removing unconjugated capture probe, after pre-amplicon, amplicon and/or label probe and capture probe are hybridized and/or etc., can cell be cleaned.
In some embodiments, for all of described method or most of step, cell is in suspension so that process.But described method is also applicable to the cell in Solid Tissue Samples (such as, histotomy) and/or is fixed on the cell in substrate (such as, microslide or other surfaces).Therefore, in the embodiment of a type, cell is in suspension in the sample comprising described cell and/or described cell is being hybridized, caught and/or be in suspension during detecting step.Such as, described cell in the sample to which with hybridizing, catch, optionally can be in suspension during cleaning and detecting step.In other embodiments, described cell is in suspension in the sample comprising described cell, and described cell is being hybridized, caught and/or be fixed in substrate during detecting step.Such as, described cell can hybridize, catch and be in suspension during optional cleaning step, and is fixed in substrate during detecting step.In other embodiments, described sample comprises histotomy.
3. the Multiple detection of nucleic acid
One aspect of the present invention provides multiple nucleic acid and measures.Therefore, a kind of embodiment of general type comprises the method detecting two or more target nucleic acids.With in upper part, describe use detect the method for single target nucleic acid.In this part, first description is used with the method for the combine detection single target nucleic acid of conventional ISH method for amplifying signal.Then description is used with the method for two or more target nucleic acids of combine detection of conventional ISH method for amplifying signal.Except using different desired specificities labels and probe, the detection of two or more target nucleic acids can be carried out by the mode identical with detecting single target nucleic acid.
In one embodiment of the invention, the method detecting single target nucleic acid is provided.In the method, the sample comprising or suspect and comprise described target nucleic acid is provided.Additionally provide: one group of two or more capture probe, wherein said capture probe can be bonded to target nucleic acid, signal produces polymer and signal amplifying probe.
Described signal produces polymer and comprises at least label probe.In a preferred embodiment, described signal generation polymer comprises label probe and amplicon.Described amplicon can be hybridized to described label probe, and can hybridize to described one group of two or more capture probe.In another preferred embodiment, described signal produce polymer comprise label probe, can hybridize to described label amplicon and can hybridize to described amplicon and the pre-amplicon that can hybridize to described one group of two or more capture probe.
Described signal amplifying probe forms by amplifying at conventional ISH signal the component used in mensuration.Such as, wherein measure in the embodiment combined with the ISH based on biotin-streptavidin (avidin), described signal amplifying probe comprises: can be bonded to the biotin molecule of label probe, avidin/the streptavidin molecule of described biotin molecule can be bonded to, and be bonded to HRP, AP or fluorophore and the other biotin molecule of described avidin/streptavidin molecule can be bonded to.
Wherein measure in the embodiment combined with the ISH based on antibody, described signal amplifying probe comprises: can be bonded to the HRP of described label probe, DNP, fluorophore or AP molecule, one or more first antibodies of described HRP, DNP, fluorophore or AP molecule can be bonded to, and be combined with HRP, polymkeric substance-HRP, AP or polymkeric substance-AP and one or more second antibody of one or more described first antibody can be bonded to.
Wherein measure in the embodiment combined with the ISH based on TSA, described signal amplifying probe comprises: can be bonded to the HRP molecule of described label probe, and can be bonded to described tyrasamine-biotin or tyrasamine-fluorophore molecule and therefore show the certification mark thing of described target nucleic acid visibly with multiple tyrasamine-biotin of described HRP molecular reaction or tyrasamine-fluorophore molecule.Described certification mark thing is the combination of avidin/streptavidin-HRP and chromogenic substrate or the combination of avidin/streptavidin-HRP and chromogenic substrate.
In the method detecting target nucleic acid, provide firstly the sample comprising or suspect and comprise described target nucleic acid.Then, described target nucleic acid hybridization is to described one group of two or more capture probe.Then, add described signal and produce polymer, and described signal produces polymer hybridization to described one group of two or more capture probe, is captured to described target nucleic acid whereby.Then, the component of described signal amplifying probe order is joined and measures in solution, and be bonded to described signal generation polymer, be captured to described target nucleic acid whereby.Then, the label in described signal amplifying probe is detected by flow cytometer or other display.The existence of described label, do not exist or measure the target nucleic acid made it possible in detection and positioning sample delicately.
In the method for detection two target nucleic acids, provide the sample comprising or suspect and comprise two target nucleic acids.Additionally provide two or more groups capture probe, often organize capture probe and comprise two or more capture probes.First group of capture probe can be hybridized to first object nucleic acid but can not hybridize to the second target nucleic acid, and second group of capture probe can be hybridized to the second target nucleic acid but can not hybridize to first object nucleic acid.Provide the first signal in addition and produce polymer and the first signal amplifying probe, and secondary signal produces polymer and secondary signal amplifying probe.
First signal produces polymer and can hybridize to first group of capture probe, but can not hybridize to second group of capture probe.Secondary signal produces polymer and can hybridize to second group of capture probe, but can not hybridize to first group of capture probe.First signal produces polymer and has the first label probe, and it is directly or by pre-amplicon and amplicon indirect hybridizing to the first group capture probe.Secondary signal produces polymer and has the second label probe, and it is directly or by pre-amplicon and amplicon indirect hybridizing to the second group capture probe.Described first label probe is different from described second label probe.
Polymer and secondary signal generation polymer is produced with different signal amplifying probe sequence notation first signals.Described two kinds of signal amplifying probes can be double-colored CISH or double-colored FISH.
At least three steps will be carried out in dual detection of nucleic acids.In a first step, mark the first signal with the first signal amplifying probe and produce polymer.In the exemplary embodiment, the first signal amplifying probe be by combine LP-HRP compound with the TSA base ISH signal that the label probe amplified connects amplifies.Implementing after method, label probe be first combined with HRP.Then, cultivate by the order of tyrasamine-biotin, streptavidin-HRP and chromogenic substrate DAB the LP-HRP compound detecting combination, thus cause producing brown signal to first object nucleic acid.In second step, block and react to prevent label from producing polymer with the secondary signal that will add in the third step for the polymeric residual labelled reagent of the first signal generation.In the third step, polymer is produced by secondary signal amplifying probe mark secondary signal.In the exemplary embodiment, implementing after method, label probe first combine with dinitrophenyl (DNP).Then, cultivate by the order of anti-DNP-AP and chromogenic substrate fast red the LP-DNP compound detecting combination, thus cause producing danger signal to first object nucleic acid.
It is also useful that said method detects for multiple nucleic acid, comprises the nucleic acid target target sequence detection of more than three kinds.Therefore, can be comprised alternatively by similar approach analysis as above or suspect comprise the third, the 4th kind, the 5th kind, the 6th kind, the 7th kind or even more kinds of nucleic acid target target cell.
4. kit
The embodiment of another kind of general type provides the kit for detecting one or more target nucleic acids.In one aspect, described kit comprise target nucleic acid, component and conventional ISH signal amplify component.In one embodiment, described kit comprises target nucleic acid, can hybridize to the capture probe group of described target nucleic acid, the signal can hybridized to capture probe group and produce polymer and can be bonded to the signal amplifying probe of described label probe.Described signal produces polymer and comprises label probe and the signal amplifying probe containing label.In some embodiments, the signal in described kit produces polymer can comprise applicable amplicon, pre-amplicon.Described kit can also comprise solid carrier.It can be any ISH signal amplifying system that the ISH signal of described kit amplifies component.Such as, it can be three kinds of ISH signal amplifying systems described in part 1.1 of the present invention.The detection of any nucleic acid that described kit is described before may be used for the present patent application, it includes, but not limited to DNA, cDNA, RNA and mRNA.
In the multiple embodiment of kit, various ingredients can be represented by two or more different subgroups.Such as, described label probe can comprise two kinds of subgroups, and it is hybridized respectively to the first and second target nucleic acids.Described signal generation polymer can comprise two kinds of different label probes, and its each direct or indirect hybridization is to the first and second capture probes.Described kit can also comprise two kinds of different signal amplifying probes, its each be bonded to the first and second label probes.By the Binding Capacity with different colours, unlike signal amplifying probe is differentiable each other.In yet another aspect, described kit comprises can block the residual sealer producing polymeric labelled reagent for the first signal, and therefore guarantees that secondary signal produces the specific binding of polymer and the second target nucleic acid.
Embodiment
Provide the following example so that the invention that (but not limiting) advocates to be described.
Pre-amplicon/amplicon ratio that the following example shows by optimizing improves further specificity that original position RNA is detected and the remarkable improvement of sensitivity how is realized with the combination of conventional ISH method for amplifying signal.
Embodiment 1. + conventional ISH signal amplifies mensuration
Can complete basic mensuration program within one day, and this program generally includes following steps.Provide containing the sample comprising multiple cells of target nucleic acid HPRT1 with suspicion.After fixing also permeability, by the cell hydridization extremely following a series of oligonucleotide probe fixed on a solid support or be in suspension.First, capture probe group is hybridized the target RNA to cell interior.Subsequently, by pre-amplicon molecular hyridization to capture probe, thus the bridge of amplicon molecular hyridization is provided for.Hybridize to pre-amplicon further by multiple amplicon molecule, such as, as many as 20 amplicon hybridization are to each pre-amplicon.Then, by multiple label probe hybridization to amplicon, such as, as many as 20 label probe hybridization are to each amplicon.
Amplified by TSA base ISH signal and strengthen signal intensity further.Then HRP is bonded to each label probe, the reagent containing tyrasamine-biotin molecule is joined and measures in solution.The label probe that HRP-combines impels multiple copies of tyrasamine-biotin to be covalently bond to the electron rich moieties of the protein of contiguous HRP-label probe binding site.Then, detect tyrasamine-biotin molecule by avidin/streptavidin-HRP, wherein avidin/streptavidin-HRP can by demonstrating brown label substrate DAB video picture.By (such as) have applicable light filter conventional fluorescent microscope or by polychrome flow cytomery signal.Compare by independent or the detection of the mRNA of low copy gene HP RT1 gene during the human breast carcinoma FFPE that+TSA base ISH signal amplifies cuts into slices.As shown in Figure 5, derive from the signal of+TSA base ISH method for amplifying signal is more independent than deriving from signal significantly stronger.
The probe groups of targeting specific mRNA sequence is designed to prevent or at utmost to reduce non-specific binding by using two " Z " probe design.The design of two " Z " capture probe is based on HPRT1 sequence and carries out prescreen to guarantee at utmost to reduce the crisscrossing with unexpected nucleotide sequence to GenBank database.In two " Z " design, two adjacent probes respectively containing target hybridization sequences, such as, T mbe significantly higher than mensuration temperature, length is the sequence of 20 to 30 bases, and pre-amplicon hybridization sequences, such as, and T mbe starkly lower than mensuration temperature, length is only the sequence of 14 bases.Therefore, during hybridizing, single capture probe can strongly and be stably bonded to target RNA, but have the T being starkly lower than and measuring temperature due to 14 base pair homology districts mand will be faint with pre-amplicon and be combined astatically.Such as, but when two capture probes exist in adjacent position, the intensity for hybridization of the merging that 28 complementary bases are right strongly and stably maintain pre-amplicon, thus makes signal amplify to occur at mensuration temperature.This two " Z " design ensure that high detection specificity, and simplifies the probe design that multiple target detects simultaneously.
Because the signal of TSA base ISH method for amplifying signal improves ability, the non-specific binding of pre-amplicon in cellular matrix during can in situ hybridization being amplified, and therefore create false positive signal.When in conjunction with multiple amplicon, also therefore size is larger in pre-amplicon design, this problem will be serious.The raising of amplifying power is is cost with the loss of binding specificity.We solve this problem by the number of the amplicon suitably reducing pre-amplicon design combination.Net result improves signal to noise ratio (S/N ratio).By ISH method for amplifying signal, particularly, the signal amplifying power of TSA base ISH method for amplifying signal compensates the loss of amplifying power.
In this mensuration, design and tested several amplicon.Pre-amplicon PREAMP1 designs in conjunction with 20 amplicons.Pre-amplicon PREAMP2 designs in conjunction with 16 amplicons.Pre-amplicon PREAMP3 designs in conjunction with 10 amplicons.Pre-amplicon PREAMP4 designs in conjunction with 5 amplicons.
Experimental result shows, and has the signal to noise ratio (S/N ratio) of improvement relative to PREAMP1, PREAMP2.In the PREAMP of all tests, PREAMP3 and PREAMP4 has best signal to noise ratio (S/N ratio) (data are not shown).
Embodiment 2. is multiple + conventional ISH signal amplifies mensuration
The predictive embodiment of multiple amplification shows the method disclosed in the present how can with high-sensitivity detection two kinds of target nucleic acids below.In order to research institute's invention disclosed is used for the possibility of in situ detection and the ability for Multiple detection thereof of low copy rna transcription basis, 18S and Her-2 is used operation mode gene.
In amplifying first, by 18S gene trap on the capture probe being designed for 18S.For the capture probe of 18S design as described in example 1 above.Then, the 18S gene order hybridization of being hybridized by capture probe is to pre-amplicon, amplicon and label probe.Then, label probe is bonded to HRP.Then, cultivate by the order of tyrasamine-biotin, streptavidin-HRP and DAB the LP-HRP compound detecting combination.The position that hybrid product is detecting target gene 18S produces brown.
Before beginning second is amplified, block the residual HRP amplified from first.In amplifying second, by Her-2 gene trap on the capture probe being designed for Her-2.For the capture probe of Her-2 design as described in example 1 above.Then, the Her-2 gene order hybridization of being hybridized by capture probe is to pre-amplicon, amplicon and label probe.Then, label probe is bonded to dinitrophenyl (DNP).Then, detect by the cultivation of anti-DNP-AP the LP-DNP combined.Then, alkaline phosphatase (AP) molecule on anti-DNP-AP compound is detected by dye reagent fast red.Hybrid product produces danger signal to target gene Her-2.
In the present embodiment, we have proved that the method disclosed in the present may be used for detection two kinds of rna transcriptions originally.Relative signal intensity may be used for the gene expression dose comparing two kinds of genes.

Claims (60)

1. detect the method for at least one target nucleic acid, described method comprises:
A () providing package contains or suspects the sample comprising described target nucleic acid;
B () provides at least one group of two or more capture probe can hybridized to described target nucleic acid;
C () provides:
I () can hybridize the amplicon to label probe;
(ii) can hybridize to described amplicon and the pre-amplicon of the group to two or more capture probes described can be hybridized, wherein said pre-amplicon: the ratio of amplicon is between 1:1-16, between 1:2-10 or between 1:2-5;
(iii) label probe, wherein said label probe is bonded to horseradish peroxidase (HRP) molecule; And
(iv) multiple tyrasamine-fluorophore molecule, or tyrasamine-biotin or tyrasamine-hapten molecule and the certification mark thing of described tyrasamine-biotin or tyrasamine-hapten molecule can be detected, wherein said tyrasamine can with described HRP molecular reaction;
D () is by the group of two or more capture probes described hybridization extremely described target nucleic acid;
E described pre-amplicon, amplicon and label probe are captured to the group of two or more capture probes described by (), thus described label probe is captured to described target nucleic acid; And
(f) detect described fluorophore existence, do not exist or measure or the certification mark thing relevant with described captured label probe.
2. method according to claim 1, wherein, described certification mark thing comprises avidin/streptavidin-HRP and chromogenic substrate or avidin/Streptavidin-Alkaline phosphatase (AP) and chromogenic substrate.
3. method according to claim 2, wherein, described chromogenic substrate is selected from: diaminobenzidine (DAB) and fast red.
4. method according to claim 1, wherein, described target nucleic acid is selected from: DNA, cDNA, RNA, mRNA, rRNA, miRNA and siRNA.
5. method according to claim 1, wherein, comprises the step captured by described target nucleic acid on solid carrier further.
6. method according to claim 1, wherein, described sample comprises cell, and described cell comprises or suspects and comprises described target nucleic acid.
7. method according to claim 1, wherein, described sample comprises cell, and described cell comprises or suspects and comprises two or more different target nucleic acids.
8. method according to claim 1, wherein, described sample comprises two or more different cells, and each in described cell comprises or suspects and comprises different target nucleic acids.
9. the method according to claim 7 or 8, wherein, utilizes double-color developing in situ hybridization (CISH) or dual FISH (FISH) to detect two kinds of different target nucleic acids.
10. method according to claim 9, wherein, utilize tyrasamine-biotin, streptavidin-HRP and DAB to implement described double-colored CISH to detect described first object nucleic acid, and utilize the anti-DNP antibody being bonded to alkaline phosphatase (AP) and fast red to detect described second target nucleic acid.
11. methods according to claim 1, wherein, described haptens is selected from dinitrophenyl (DNP), digoxin, trinitrophenyl (TNP) or fluorophore.
12. methods according to claim 1, wherein, provide multiple tyrasamine-fluorophore molecule.
13. methods according to claim 1, wherein, provide multiple tyrasamine-biotin molecule and the certification mark thing that can detect described tyrasamine-biotin molecule.
14. methods according to claim 13, wherein, described certification mark thing comprises avidin/streptavidin.
15. methods according to claim 14, wherein, described avidin/streptavidin is bonded to HRP, polymkeric substance-HRP, AP, polymkeric substance-AP or fluorophore.
16. methods according to claim 15, wherein, described certification mark thing comprises chromogenic substrate.
17. methods according to claim 16, wherein, described chromogenic substrate is selected from DAB and fast red.
18. methods according to claim 16, wherein, described certification mark thing comprises avidin/streptavidin-HRP.
19. methods according to claim 18, wherein, described certification mark thing comprises avidin/streptavidin-HRP and DAB.
20. methods according to claim 16, wherein, described certification mark thing comprises avidin/streptavidin-AP.
21. methods according to claim 20, wherein, described certification mark thing comprises avidin/streptavidin-AP and fast red.
22. methods according to claim 1, wherein, provide multiple tyrasamine-hapten molecule and the certification mark thing that can detect described tyrasamine-hapten molecule.
23. methods according to claim 22, wherein, described certification mark thing comprises anti-hapten antibody.
24. methods according to claim 23, wherein, described certification mark thing comprises second antibody further, and wherein said second antibody can be incorporated into described anti-hapten antibody and wherein said second antibody is bonded to HRP, polymkeric substance-HRP, AP, polymkeric substance-AP or fluorophore.
25. methods according to claim 24, wherein, described second antibody is bonded to fluorophore.
26. methods according to claim 24, wherein, described certification mark thing comprises chromogenic substrate.
27. methods according to claim 26, wherein, described chromogenic substrate is selected from DAB and fast red.
28. methods according to claim 26, wherein, described second antibody is bonded to HRP.
29. methods according to claim 28, wherein, described chromogenic substrate is DAB.
30. methods according to claim 26, wherein, described second antibody is bonded to AP.
31. methods according to claim 30, wherein, described chromogenic substrate is fast red.
32. 1 kinds of kits, comprise:
A () can hybridize at least one group of two or more capture probe to target nucleic acid;
B () can hybridize the amplicon to label probe;
C () can hybridize to described amplicon and can hybridize the pre-amplicon of the group to two or more capture probes described, wherein said pre-amplicon: the ratio of amplicon is between 1:1-16, between 1:2-10 or between 1:2-5;
(d) label probe, wherein said label probe is bonded to HRP molecule; And
(e) multiple tyrasamine-fluorophore molecule, or tyrasamine-biotin or tyrasamine-hapten molecule and the certification mark thing of described tyrasamine-biotin or tyrasamine-hapten molecule can be detected, wherein said tyrasamine can with described HRP molecular reaction.
33. kits according to claim 32, wherein, described certification mark thing comprises avidin/streptavidin-HRP and chromogenic substrate or avidin/streptavidin-AP and chromogenic substrate.
34. kits according to claim 33, wherein, described chromogenic substrate is selected from: DAB and fast red.
35. kits according to claim 32, wherein, described target nucleic acid is selected from: DNA, cDNA, RNA, mRNA, rRNA, miRNA and siRNA.
36. kits according to claim 32, wherein, comprise described target nucleic acid further.
37. kits according to claim 32, wherein, comprise two groups of two or more capture probes, often organize capture probe and can hybridize to different target nucleic acids.
38. kits according to claim 36 or 37, wherein, described kit comprises reagent for double-color developing in situ hybridization (CISH) or dual FISH (FISH) for the different target nucleic acid of detection two kinds.
39. according to kit according to claim 38, wherein, described double-colored CISH pack is containing tyrasamine-biotin, streptavidin-HRP and DAB for the described first object nucleic acid of detection, and the anti-DNP antibody being bonded to alkaline phosphatase and fast red is for described second target nucleic acid of detection.
40. kits according to claim 32, wherein, described haptens is selected from dinitrophenyl (DNP), digoxin, trinitrophenyl (TNP) or fluorophore.
41. kits according to claim 32, wherein, described kit comprises multiple tyrasamine-fluorophore molecule.
42. kits according to claim 32, wherein, described kit comprises multiple tyrasamine-biotin molecule and can detect the certification mark thing of described tyrasamine-biotin molecule.
43. kits according to claim 42, wherein, described certification mark thing comprises avidin/streptavidin.
44. kits according to claim 43, wherein, described avidin/streptavidin is bonded to HRP, polymkeric substance-HRP, AP, polymkeric substance-AP or fluorophore.
45. kits according to claim 44, wherein, described certification mark thing comprises chromogenic substrate.
46. kits according to claim 45, wherein, described chromogenic substrate is selected from DAB and fast red.
47. kits according to claim 45, wherein, described certification mark thing comprises avidin/streptavidin-HRP.
48. kits according to claim 47, wherein, described certification mark thing comprises avidin/streptavidin-HRP and DAB.
49. kits according to claim 45, wherein, described certification mark thing comprises avidin/streptavidin-AP.
50. kits according to claim 49, wherein, described certification mark thing comprises avidin/streptavidin-AP and fast red.
51. kits according to claim 32, wherein, described kit comprises multiple tyrasamine-hapten molecule and can detect the certification mark thing of described tyrasamine-hapten molecule.
52. kits according to claim 51, wherein, described certification mark thing comprises anti-hapten antibody.
53. kits according to claim 52, wherein, described certification mark thing comprises second antibody further, and wherein said second antibody can be incorporated into described anti-hapten antibody and wherein said second antibody is bonded to HRP, polymkeric substance-HRP, AP, polymkeric substance-AP or fluorophore.
54. kits according to claim 53, wherein, described second antibody is bonded to fluorophore.
55. kits according to claim 53, wherein, described certification mark thing comprises chromogenic substrate.
56. kits according to claim 55, wherein, described chromogenic substrate is selected from DAB and fast red.
57. kits according to claim 55, wherein, described second antibody is bonded to HRP.
58. kits according to claim 57, wherein, described chromogenic substrate is DAB.
59. kits according to claim 55, wherein, described second antibody is bonded to AP.
60. kits according to claim 59, wherein, described chromogenic substrate is fast red.
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